Crystal structure and structural disorder of Ba3MgSi2O8 were reinvestigated by laboratory X-ray powder diffraction. The title compound was found to be trigonal with space group P3m1, Z=1, and unit-cell dimensions a=0.561 453(4) nm, c=0.727 629(4) nm, and V=0.198 641(2) nm3. The initial structural model used for structure refinement was taken from that of glaserite (K3NaS2O8) and modified by a split-atom model. In the split-atom model, one of the two types of Ba sites and that of SiO4 tetrahedra were, respectively, positionally and orientationally disordered. The new crystal structure and structural disorder were refined by the Rietveld method. The maximum-entropy-method-based pattern fitting (MPF) method was used to confirm the validity of the split-atom model, in which conventional structure bias caused by assuming intensity partitioning was minimized. The final reliability indices calculated from MPF were Rwp=6.52%, S=1.36, Rp=4.84%, RB=0.97%, and RF=0.52%. Details of the disorder structure of Ba3MgSi2O8 are shown in the three-dimensional and two-dimensional electron-density distribution maps determined by MPF.